Antigen

Antigen Class

TFs and others

Antigen

Nr3c1

Cell type

Cell type Class

Liver

Cell type

Hepatocytes

MeSH Description

The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.

Sample

source_name

hepatocytes

tissue

liver

strain

C57BL/6JOlaHsd

antibody

GR (Cell Signaling Technologies cat# 3660)

cell type

hepatocytes

Sequenced DNA Library

library_name

GSM5696914

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

RNA: Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer's protocol. ChIP: cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125M glycine. Crosslinked samples were washed in PBS, resuspended in ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) and sonicated (Bioruptor, Diagenode) to release 100-1000 bp fragments. Antibodies (4 μg per 300 μg chromatin) against H3K27ac (Active motif #39133) or GR (CST #3660) were conjugated to magnetic beads (Sera-Mag, Merck #GE17152104010150) for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates over night at 4°C. Immunocomplexes were washed sequentially with the following buffers: low-salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2mM EDTA, 20mM Tris-HCl pH8, 500mM NaCl), low salt buffer and TE buffer (10mMTris-HCl, 1mM EDTA pH8). Chromatin was de-proteinized with proteinase K (Hy Labs EPR9016) for 2 h at 55°C and de-crosslinked over night at 65°C. DNA was subsequently phenol-chloroform purified and ethanol precipitated For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

Sequencing Platform

instrument_model

NextSeq 500

mm10

Number of total reads

36053368

Reads aligned (%)

92.8

Duplicates removed (%)

23.5

Number of peaks

483 (qval < 1E-05)

mm9

Number of total reads

36053368

Reads aligned (%)

92.5

Duplicates removed (%)

23.5

Number of peaks

469 (qval < 1E-05)